Landscape of RNA polyadenylation in E. coli
2015 (English)Manuscript (preprint) (Other academic)
Polyadenylation is involved in degradation and quality control of bacterial RNAs. We used a combination of 5’-tagRACE and RNA-seq to analyse the total RNA content from wild-type strain and from mutant deficient for poly(A)polymerase. We determined that 157 mRNAs were affected as well as non-coding transcripts, up- and downregulated in the mutant when compared to the wild-type strain. Antisense RNAs were also detected and differentially affected by polyadenylation.
Our results clearly reveal a correlation between the RNA folding energy and the requirement of polyadenylation to achieve the RNA decay. A new algorithm was developed to detect in both strains posttranscriptional modifications based on unmappable 3’-ends to analyse their position and composition. Therefore, any RNA 3'-end can be polyadenylated addressing them to the exoribonucleolytic machinery which is essential to degrade structured RNAs. Importantly, poly(A)polymerase was also upregulating the expression of genes related with the entire FliA regulon and numerous membrane transporters while downregulating the expression of the antigen 43 (flu), numerous sRNAs, antisense transcripts, REP sequences with the accumulation of numerous RNA fragments resulting from the processing of entire transcripts. Altogether we show here that polyadenylation has a broader spectrum of action than was suspected until now.
Place, publisher, year, edition, pages
Polyadenylation, degradation, poly(A)polymerase, pcnB deficient mutant
Microbiology Bioinformatics (Computational Biology) Genetics
Research subject Biological Physics
IdentifiersURN: urn:nbn:se:kth:diva-173328OAI: oai:DiVA.org:kth-173328DiVA: diva2:852512
QS 20152015-09-092015-09-092016-02-02Bibliographically approved